RetrogeneDB ID: retro_nleu_661

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397269.1:5780143..5781069(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: FAM175A
• Ensembl ID: ENSNLEG00000009133
• Aliases: None
• Description: None

Sequence

>retro_nleu_661
ATTACTGTTTCCCAAATGGATGATGTTGAAGTTGTTTATACAATTGACATTCAGAAATATATTCCATGTTATCAGTTTTT
TAGCTTTTATACTTCTTCAGGTGAAGTAAATGAGCAAGCACTGAAGAAAATATTATCAAATTCACAAAGAATGTGGTAGG
TTGGTACAAATTCCCTCATCATTCAGATCAGATCATGACGTTTAGAGAAAGGCTGCTTCACAAAAACTTGCAGGAGCATC
TTTCAAACCAAGACCTTGTTTTTCTGCTATGAACAAGTATAATAACAGAAAGCCGCTCTACTCATCGACTCGAACATGCC
TTATATAAACCTCAAAAAGGACTTTTTCACAGGGTACCTTTAGTGGTTGCCAATCTGGGCATGTCTGAACAACTAGATTG
TAAAACTGTATCAGGTTCCTGTATGTCCACTGGTTTTAGCCGAGCAGTACAAACACACAGCTCTAATTTTTTTTGAAGAA
GATGTATCCTTAAAGAAGGTACATAAGATAAATGAAATGTATGCTTCATTACAAGAGGAATTAAAGAGTATATGCAAAAA
AGTGGAAGACAGTGAATAAGCAGTAGATAAACTAGTAAAGGATGTAAACAGATTAAAACAAGAAATTGAAAAAAGGAGAC
GAGCCCAGATTCAGGCAGCACGAGAGAAGAGCATCCAAAAACCCTCAGGAGAACATTTTTCTTTGTCAACCATTAAGGAC
CTTTTTTCCAGATTGTGAATTTCTTCATTCATGTGTTATGTCTTTAAAACAATAGACATGTTTCTAAAGGTAGCTCTAAC
AACCACTACCATCTCGATGTAGTAGACAATCTGACCTTAATGGTGGAAAACACTGACATTCCTGAAGCTAGTCCAGCTAG
TACACCACAAATGGTTAAGCATAAAGCCTTAGACTTAGATGGCAGA

Alignment

ORF - retro_nleu_661 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.8 %
• Parental protein coverage: 75.79 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  ITDSQMDDVEVVYTIDIQKYIPCYQLFSFYNSSGEVNEQALKKILSNVK-KHVVGWYKFRRHSDQIMTFR
          IT.SQMDDVEVVYTIDIQKYIPCYQ.FSFY.SSGEVNEQALKKILSN...K.VVGWYKF..HSDQIMTFR
Retrocopy ITVSQMDDVEVVYTIDIQKYIPCYQFFSFYTSSGEVNEQALKKILSNSQ<KNVVGWYKFPHHSDQIMTFR

Parental  ERLLHKNLQEHFSNQDLVFLLLTPSIITESCSTHRLEHSLYKPQKGLFHRVPLVVANLGMSEQLGYKTVS
          ERLLHKNLQEH.SNQDLVFLL.T.SIITES.STHRLEH.LYKPQKGLFHRVPLVVANLGMSEQL..KTVS
Retrocopy ERLLHKNLQEHLSNQDLVFLL*T-SIITESRSTHRLEHALYKPQKGLFHRVPLVVANLGMSEQLDCKTVS

Parental  GSCMSTGFHQAVQTHSSKFF-EEDGSLKEVHKINEMYASLQEELKSICKKVEDSEQAVDKLVKDVNRLKR
          GSCMSTGF..AVQTHSS....EED.SLK.VHKINEMYASLQEELKSICKKVEDSE.AVDKLVKDVNRLK.
Retrocopy GSCMSTGFSRAVQTHSSXXX>EEDVSLKKVHKINEMYASLQEELKSICKKVEDSE*AVDKLVKDVNRLKQ

Parental  EIKKRRRAQIQAAREKNIQKDPQENIFLCQALRTFF-PNSEFLHSCVMSLK-NRHVSKSSCNYNHHLDVV
          EI.KRRRAQIQAAREK.IQK.P....F........F.P..EFLHSCVMSLK.NRHVSK.S.N...HLDVV
Retrocopy EIEKRRRAQIQAAREKSIQK-PSGEHFSLSTIKDLF>PDCEFLHSCVMSLK>NRHVSKGSSNNHYHLDVV

Parental  DNLTLMVEHTDIPEASPASTPQIIKHKALDLDDR
          DNLTLMVE.TDIPEASPASTPQ..KHKALDLD.R
Retrocopy DNLTLMVENTDIPEASPASTPQMVKHKALDLDGR

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Nomascus leucogenys was not studied using RNA-Seq expression data.

ChIP-Seq

Nomascus leucogenys was not studied using ChIP-Seq data.

EST

Nomascus leucogenys was not studied using EST data.

TSS

Nomascus leucogenys was not studied using FANTOM5 data.

Lab

retro_nleu_661 was not experimentally validated.

Homology

Retrocopy orthology:

Nomascus leucogenys does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013241	1 retrocopy	retro_chof_2580,
Homo sapiens	ENSG00000163322	1 retrocopy	retro_hsap_4024,
Macaca mulatta	ENSMMUG00000015357	2 retrocopies	retro_mmul_1499, retro_mmul_2320,
Nomascus leucogenys	ENSNLEG00000009133	2 retrocopies	retro_nleu_1198, retro_nleu_661 ,
Pongo abelii	ENSPPYG00000014898	2 retrocopies	retro_pabe_2208, retro_pabe_3301,
Pan troglodytes	ENSPTRG00000023645	2 retrocopies	retro_ptro_1911, retro_ptro_2728,